A Chemical Biology Platform to Develop Small Molecule Probes for Bromodomains

Abstract

Bromodomain epigenetic reader proteins play crucial roles in the pathogenesis of diseases ranging from inflammation to cancer. Small molecule inihibitors have engendered a nuanced understanding of the role of BET subfamily bromodomains in multiple diseases. Here, platforms were established to facilitate chemical probe development for the remaining ~50 bromodomains with a concentrated focus on establishing a pipeline for the discovery of CBP bromodomain inhibitors. CBP is a large bromodomain-containing transcriptional co-activator involved in cell proliferation and growth, cellular differentiation and development, cognitive function, and cell adhesion. It is involved in the pathogenesis of cancer, in particular hematologic diseases. A high-throughput biochemical assay, cellular viability assay, and cellular target engagement assay were established in order to screen and validate small molecule inhibitors of the CBP bromodomain. A family-wide bromodomain profiling platform (BROMOscan) was established and fully validated to provide broad quantitative binding affinity and selectivity information. Using this platform, novel small molecule inhibitors for non-BET domains were discovered. Moreover, a LRRK2 kinase inhibitor with potent bromodomain cross-reactivity was identified and optimized. Using BROMOscan and the CBP bromodomain assays deeloped here, a dually functioning kinase-bromodomain inhibitor was discovered that was potent and selective for CBP.